Crystal structure of D-stereospecific amidohydrolase from Streptomyces sp. 82F2 - insight into the structural factors for substrate specificity

State-of-the-art strategies and research advances for the biosynthesis of D-amino acids

D-amino acids (D-AAs) are the enantiomeric counterparts of L-amino acids (L-AAs) and important functional factors with a wide variety of physiological activities and applications in the food manufacture industry. Some D-AAs, such as D-Ala, D-Leu, and D-Phe, have been favored by consumers as sweeteners and fragrances because of their unique flavor. The biosynthesis of D-AAs has attracted much attention in recent years due to their unique advantages. In this review, we comprehensively analyze the structure-function relationships, biosynthesis pathways, multi-enzyme cascade and whole-cell catalysis for the production of D-AAs. The state-of-the-art strategies, including immobilization, protein engineering, and high-throughput screening, are summarized. Future challenges and perspectives of strategies-driven by bioinformatics technologies and smart computing technologies, as well as enzyme immobilization, are also discussed. These new approaches will promote the commercial production and application of D-AAs in the food industry by optimizing the key enzymes for industrial biocatalysts.

Acetylation of amines and alcohols catalyzed by acetylcholinesterase from Pseudomonas aeruginosa PAO1

Acetylcholinesterase (AChE) from Pseudomonas aeruginosa PAO1 has a catalytic Ser residue in its active site. In this study, we examined the aminolysis and alcoholysis reactions of AChE that occurred alongside its hydrolysis reaction. The recombinant AChE recognized ethyl acetate as a substrate. Therefore, we evaluated acetylation of the amine and hydroxyl group by AChE, using acetylcholine and ethyl acetate as the acetyl donor. AChE recognized diaminoalkanes with 4- to 12-carbon chains and aminoalcohols with 4- to 8-carbon chains as acetyl acceptors, resulting in their acetylated products. In the acetylation of 1,6-diaminohexane, AChE preferentially used ethyl acetate as the acetyl donor above pH 8.0 and the efficiency increased with increasing pH. In contrast, the acetylation of 6-amino-1-hexanol was efficient with acetylcholine as the acetyl donor in the pH range of 4-10. In addition, acetylated 6-amino-1-hexanol was decomposed by AChE. The kinetic study indicated that the acetyl donor and acceptor are competitively recognized by AChE as substrates.

Systematic Structure-Based Search for Ochratoxin-Degrading Enzymes in Proteomes from Filamentous Fungi

(1) Background: ochratoxins are mycotoxins produced by filamentous fungi with important implications in the food manufacturing industry due to their toxicity. Decontamination by specific ochratoxin-degrading enzymes has become an interesting alternative for the treatment of contaminated food commodities. (2) Methods: using a structure-based approach based on homology modeling, blind molecular docking of substrates and characterization of low-frequency protein motions, we performed a proteome mining in filamentous fungi to characterize new enzymes with potential ochratoxinase activity. (3) Results: the proteome mining results demonstrated the ubiquitous presence of fungal binuclear zinc-dependent amido-hydrolases with a high degree of structural homology to the already characterized ochratoxinase from Aspergillus niger. Ochratoxinase-like enzymes from ochratoxin-producing fungi showed more favorable substrate-binding pockets to accommodate ochratoxins A and B. (4) Conclusions: filamentous fungi are an interesting and rich source of hydrolases potentially capable of degrading ochratoxins, and could be used for the detoxification of diverse food commodities.

Computational study on the polymerization reaction of d-aminopeptidase for the synthesis of d-peptides

Almost all natural proteins are composed exclusively of l-amino acids, and this chirality influences their properties, functions, and selectivity. Proteases can recognize proteins composed of l-amino acids but display lower selectivity for their stereoisomers, d-amino acids. Taking this as an advantage, d-amino acids can be used to develop polypeptides or biobased materials with higher biostability. Chemoenzymatic peptide synthesis is a technique that uses proteases as biocatalysts to synthesize polypeptides, and d-stereospecific proteases can be used to synthesize polypeptides incorporating d-amino acids. However, engineered proteases with modified catalytic activities are required to allow the incorporation of d-amino acids with increased efficiency. To understand the stereospecificity presented by proteases and their involvement in polymerization reactions, we studied d-aminopeptidase. This enzyme displays the ability to efficiently synthesize poly d-alanine-based peptides under mild conditions. To elucidate the mechanisms involved in the unique specificity of d-aminopeptidase, we performed quantum mechanics/molecular mechanics simulations of its polymerization reaction and determined the energy barriers presented by the chiral substrates. The enzyme faces higher activation barriers for the acylation and aminolysis reactions with the l-stereoisomer than with the d-substrate (10.7 and 17.7 kcal mol⁻¹ higher, respectively). The simulation results suggest that changes in the interaction of the substrate with Asn155 influence the stereospecificity of the polymerization reaction.

We studied the molecular mechanism of d-aminopeptidase for the synthesis of polypeptides incorporating d-amino acids.

Active site pocket of Streptomycesd-stereospecific amidohydrolase has functional roles in aminolysis activity

d-Stereospecific amidohydrolase from Streptomyces sp. 82F2 (DAH) recognizes d-amino acyl ester derivatives as substrates and catalyzes hydrolysis and aminolysis to yield d-amino acids and d-amino acyl peptides or amide derivatives, respectively. Crystallographic analysis has revealed that DAH possesses a large cavity with a small pocket at the bottom. Because the pocket is close to the catalytic center and is thought to interact with substrates, we examined the function of the eight residues that form the pocket in terms of substrate recognition and aminolysis via mutational analysis. Formation of the acyl-enzyme intermediate and catalysis of aminolysis by DAH were changed by substitutions of selected residues with Ala. In particular, I338A DAH exhibited a significant increase in the condensation product of Ac-d-Phe methyl ester and 1,8-diaminooctane (Ac-d-Phe-1,8-diaminooctane) compared with the wild-type DAH. A similar effect was observed by the mutation of Ile338 to Gly and Ser. The pocket shapes and local flexibility of the mutants I338G, I338A, and I338S are thought to resemble each other. Thus, changes in the shape and local flexibility of the pocket of DAH by mutation presumably alter substrate recognition for aminolysis.